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Well, however is most convenient and makes most sense for your application, of course. Just remember that it's not a good idea to store more than 10 thousand files on Linux servers in a single folder, it's even better to simply not store more than thousand per folder.

To do this, you should simply create subfolders that minimize the risk of such a large number of files. You can separate them in subfolders (for example, storing a file alphabet.pdf in /alp/ subfolder) or store them based on creation dates.